Variant report

Variant	rs8098730
Chromosome Location	chr18:12884676-12884677
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12882099-12885668	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr18:12883006-12884887	Raji	blood:	n/a	n/a
3	POLR2A	chr18:12883379-12884765	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr18:12883095-12884708	MCF-7	breast:	n/a	n/a
5	POLR2A	chr18:12884676-12884682	K562	blood:	n/a	n/a
6	ELK1	chr18:12883645-12884893	GM12878	blood:	n/a	n/a
7	EBF1	chr18:12884416-12884678	GM12878	blood:	n/a	chr18:12884550-12884560
8	MYC	chr18:12883417-12884786	MCF10A-Er-Src	breast:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
9	MXI1	chr18:12882814-12886050	GM12878	blood:	n/a	n/a
10	MYC	chr18:12883034-12884687	NB4	blood:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
11	NRF1	chr18:12883290-12884928	SK-N-SH	brain:	n/a	chr18:12884252-12884261 chr18:12884152-12884163 chr18:12883915-12883926 chr18:12883830-12883841 chr18:12883912-12883926 chr18:12883529-12883543 chr18:12884225-12884239 chr18:12883827-12883841 chr18:12884228-12884239 chr18:12884228-12884242 chr18:12884228-12884237 chr18:12884167-12884178 chr18:12884228-12884239 chr18:12884230-12884239
12	MAX	chr18:12883572-12884702	H1-hESC	embryonic stem cell:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
13	POLR2A	chr18:12882559-12886033	GM12891	blood:	n/a	n/a
14	MAX	chr18:12883426-12884774	ECC-1	luminal epithelium:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
15	EP300	chr18:12883645-12884854	GM12878	blood:	n/a	chr18:12884142-12884158
16	CREB1	chr18:12883236-12884730	HepG2	liver:	n/a	n/a
17	TCF12	chr18:12884375-12884784	GM12878	blood:	n/a	n/a
18	POLR2A	chr18:12883058-12884733	GM19193	blood:	n/a	n/a
19	TAF1	chr18:12883433-12884796	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr18:12882859-12886028	GM12878	blood:	n/a	n/a
21	EP300	chr18:12883393-12884725	GM12878	blood:	n/a	chr18:12884142-12884158
22	USF2	chr18:12884423-12884721	GM12878	blood:	n/a	n/a
23	SPI1	chr18:12884391-12884866	GM12878	blood:	n/a	n/a
24	POLR2A	chr18:12883277-12884851	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYC	chr18:12882688-12884769	K562	blood:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
26	POLR2A	chr18:12884378-12886072	GM12878	blood:	n/a	n/a
27	POLR2A	chr18:12882686-12886052	GM12878	blood:	n/a	n/a
28	MAX	chr18:12883147-12884850	GM12878	blood:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
29	POLR2A	chr18:12882835-12884790	SK-N-MC	brain:	n/a	n/a
30	ZNF143	chr18:12883666-12884775	GM12878	blood:	n/a	chr18:12884171-12884181 chr18:12883745-12883763
31	ELF1	chr18:12883511-12884693	GM12878	blood:	n/a	n/a
32	POLR2A	chr18:12883257-12884715	H1-hESC	embryonic stem cell:	n/a	n/a
33	ZBTB7A	chr18:12884371-12884720	ECC-1	luminal epithelium:	n/a	chr18:12884464-12884471
34	POLR2A	chr18:12883166-12884738	GM12891	blood:	n/a	n/a
35	MAZ	chr18:12882662-12885166	IMR90	lung:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
36	MXI1	chr18:12882164-12885188	SK-N-SH	brain:	n/a	n/a
37	MAX	chr18:12883225-12884728	ECC-1	luminal epithelium:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
38	EBF1	chr18:12883735-12886127	GM12878	blood:	n/a	chr18:12884550-12884560 chr18:12885778-12885789 chr18:12885801-12885812
39	POLR2A	chr18:12884384-12884720	PANC-1	pancreas:	n/a	n/a
40	TBL1XR1	chr18:12883670-12885115	GM12878	blood:	n/a	n/a
41	RCOR1	chr18:12883674-12884794	GM12878	blood:	n/a	n/a
42	POLR2A	chr18:12883415-12884852	Hela-S3	cervix:	n/a	n/a
43	SPI1	chr18:12884385-12884730	GM12891	blood:	n/a	n/a
44	SPI1	chr18:12884431-12884683	K562	blood:	n/a	n/a
45	BHLHE40	chr18:12883664-12884684	K562	blood:	n/a	n/a
46	RELA	chr18:12883563-12884867	GM10847	blood:	n/a	n/a
47	SPI1	chr18:12884383-12884717	GM12878	blood:	n/a	n/a
48	SIN3A	chr18:12883170-12884851	H1-hESC	embryonic stem cell:	n/a	chr18:12884217-12884226 chr18:12883665-12883678
49	CHD1	chr18:12884549-12884718	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr18:12883504-12884703	HepG2	liver:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266

No.	Distal block	Cell Line	Cell type
1	chr15:65596946..65598700-chr18:12882626..12885488,2	MCF-7	breast:
2	chr18:12774117..12776643-chr18:12883699..12885836,3	K562	blood:
3	chr18:12880282..12885478-chr18:12946145..12950206,8	K562	blood:
4	chr18:12882771..12885367-chr18:12946819..12949664,2	MCF-7	breast:
5	chr11:59436284..59437132-chr18:12883857..12884750,2	Hela-S3	cervix:
6	chr18:12760116..12762309-chr18:12883836..12885442,2	K562	blood:
7	chr17:40272993..40273808-chr18:12884016..12884888,2	Hela-S3	cervix:
8	chr1:145382262..145383113-chr18:12883770..12884685,2	Hela-S3	cervix:
9	chr12:105501007..105501649-chr18:12884012..12884801,2	Hela-S3	cervix:
10	chr10:101190701..101191272-chr18:12884017..12884694,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEH1L-5	chr18:12884514-12885555	NONHSAT058399

Variant related genes	Relation type
PTPN2	TF binding region
ENSG00000260302	Chromatin interaction
ENSG00000108773	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000224934	Chromatin interaction
ENSG00000166889	Chromatin interaction
ENSG00000201466	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000255355	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs2032174	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs2292758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2847288	0.88[JPT][hapmap]
rs34846641	0.81[AFR][1000 genomes]
rs3826556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs45579734	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4797707	0.82[ASN][1000 genomes]
rs4797708	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507304	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs513185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56384328	0.88[ASN][1000 genomes]
rs578377	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58200120	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59471125	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs607906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs60803113	0.88[ASN][1000 genomes]
rs622717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs637643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505769	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs670671	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs683468	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7234029	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7238238	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7241016	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7241650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872144	0.87[ASN][1000 genomes]
rs73950681	0.83[ASN][1000 genomes]
rs73950683	0.85[ASN][1000 genomes]
rs73950684	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73950685	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8083786	0.93[AFR][1000 genomes]
rs8084365	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9954778	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9959061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9961827	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9961931	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9966378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv909407	chr18:12877060-12917703	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	n/a
7	esv3433183	chr18:12883052-12885400	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12882200-12885000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr18:12882200-12885000	Active TSS	A549	lung
3	chr18:12882200-12885000	Active TSS	HMEC	breast
4	chr18:12882200-12885000	Active TSS	NHLF	lung
5	chr18:12882400-12885000	Active TSS	GM12878-XiMat	blood
6	chr18:12882400-12885200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr18:12882400-12885600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr18:12882600-12884800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr18:12882600-12884800	Active TSS	Psoas Muscle	Psoas
10	chr18:12882600-12885000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:12882600-12885000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:12882600-12885000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:12882600-12885000	Active TSS	Fetal Stomach	stomach
14	chr18:12882600-12885000	Active TSS	NHDF-Ad	bronchial
15	chr18:12882800-12884800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr18:12882800-12884800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr18:12882800-12884800	Active TSS	Stomach Mucosa	stomach
18	chr18:12882800-12885000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr18:12882800-12885000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr18:12882800-12885000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr18:12882800-12885000	Active TSS	Fetal Intestine Small	intestine
22	chr18:12882800-12885000	Active TSS	Placenta	Placenta
23	chr18:12882800-12885200	Active TSS	Colonic Mucosa	Colon
24	chr18:12883000-12884800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr18:12883000-12884800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:12883000-12884800	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr18:12883000-12884800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr18:12883000-12884800	Active TSS	Colon Smooth Muscle	Colon
29	chr18:12883000-12884800	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr18:12883000-12884800	Active TSS	Esophagus	oesophagus
31	chr18:12883000-12884800	Active TSS	Fetal Kidney	kidney
32	chr18:12883000-12884800	Active TSS	Gastric	stomach
33	chr18:12883000-12884800	Active TSS	Ovary	ovary
34	chr18:12883000-12884800	Active TSS	Pancreas	Pancrea
35	chr18:12883000-12884800	Active TSS	Small Intestine	intestine
36	chr18:12883000-12884800	Active TSS	K562	blood
37	chr18:12883000-12884800	Active TSS	NHEK	skin
38	chr18:12883000-12885000	Active TSS	Aorta	Aorta
39	chr18:12883000-12885000	Active TSS	Fetal Intestine Large	intestine
40	chr18:12883000-12885000	Active TSS	Right Ventricle	heart
41	chr18:12883200-12884800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr18:12883200-12884800	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr18:12883200-12884800	Active TSS	Liver	Liver
44	chr18:12883200-12884800	Active TSS	Brain Angular Gyrus	brain
45	chr18:12883200-12884800	Active TSS	Brain Anterior Caudate	brain
46	chr18:12883200-12884800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr18:12883200-12884800	Active TSS	Fetal Lung	lung
48	chr18:12883200-12884800	Active TSS	Left Ventricle	heart
49	chr18:12883200-12884800	Active TSS	Lung	lung
50	chr18:12883200-12884800	Active TSS	Sigmoid Colon	Sigmoid Colon

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